7V3O | pdb_00007v3o

The structure of Se-SoBcmB with Fe(II)and AKG

PDB DOI: https://doi.org/10.2210/pdb7V3O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces ossamyceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-08-10 Released: 2023-02-15
Deposition Author(s): Wu, L., Zhou, J.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.200 (Depositor), 0.203 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis

He, J.B., Wu, L., Wei, W., Meng, S., Liu, Z.T., Wu, X., Pan, H.X., Yang, S., Liang, Y., Zhou, J., Tang, G.L.

(2023) Nat Catal 6: 637-648

DOI: https://doi.org/10.1038/s41929-023-00987-4

Macromolecule Content

Total Structure Weight: 37.75 kDa
Atom Count: 2,369
Modeled Residue Count: 277
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe/2OG dependent dioxygenase	A	328	Streptomyces ossamyceticus	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YA87 (Streptomyces ossamyceticus) Explore A0A9Y2YA87 Go to UniProtKB: A0A9Y2YA87
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9Y2YA87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG (Subject of Investigation/LOI) Query on AKG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain E [auth A]	B [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.200 (Depositor), 0.203 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.62	α = 90
b = 101.62	β = 90
c = 130.57	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-09-04
Changes: Data collection, Database references
Version 1.2: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.